We propose a joint multi-polarization-effect tracking and equalization method based on two extended Kalman filters, which can cope with state of polarization (SOP) tracing, polarization demultiplexing, equalization for polarization dependent loss (PDL) and polarization mode dispersion (PMD) in PDM-M-QAM coherent optical communication system. The mathematical model of the proposed method is given and analyzed in detail. Through simulation, the proposed method is proved to be very effective in a 28 Gbaud/s PDM-16QAM system. With the proposed method, SOP tracing speed is up to 110 Mrad/s for azimuth angle and 1200 krad/s for phase angle, respectively, and PDL and PMD can be equalized simultaneously in the values of 10 dB and more than half of the symbol period.